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After Mr. Trump told his staff on Sept. 5 to address the matter, Mr. Mulvaney called Mr. Ross, who was in Greece traveling for meetings. Mr. Ross then called Neil Jacobs, the acting administrator of NOAA, at home around 3 a.m. Friday, Washington time, and instructed him to clear up the agency’s contradiction of the president, according to three people informed about the discussions.

Dr. Jacobs objected to the demand and was told that the political appointees at NOAA would be fired if the situation were not fixed, according to the three individuals, who requested anonymity because they were not authorized to discuss the episode. The political staff at an agency typically includes a handful of top officials, such as Dr. Jacobs, and their aides. They are appointed by the administration currently in power, as opposed to career government employees, who remain as administrations come and go.

The statement NOAA ultimately issued later on Friday faulted the Birmingham office for a tweet that “spoke in absolute terms that were inconsistent with probabilities from the best forecast products available at the time.”

Dr. Jacobs has since sought to reassure his work force and the broader scientific community concerned about political interference.

“This administration is committed to the important mission of weather forecasting,” Dr. Jacobs said at a weather conference on Tuesday in Huntsville, Ala. “There is no pressure to change the way you communicate or forecast risk in the future.”

In the speech, Dr. Jacobs praised Mr. Trump, calling him “genuinely interested in improving weather forecasts,” and echoed the president’s position that Dorian initially threatened Alabama. “At one point, Alabama was in the mix, as was the rest of the Southeast.”

He also said he still had faith in the Birmingham office. “The purpose of the NOAA statement was to clarify the technical aspects of the potential impacts of Dorian,” Dr. Jacobs said. “What it did not say, however, is that we understand and fully support the good intent of the Birmingham weather forecast office, which was to calm fears in support of public safety.”